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* Residue conservation analysis
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Enzyme class:
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Chains A, B:
E.C.3.2.2.22
- rRNA N-glycosylase.
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Reaction:
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Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
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DOI no:
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Proteins
43:319-326
(2001)
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PubMed id:
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2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.
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J.M.Pascal,
P.J.Day,
A.F.Monzingo,
S.R.Ernst,
J.D.Robertus,
R.Iglesias,
Y.Pérez,
J.M.Férreras,
L.Citores,
T.Girbés.
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ABSTRACT
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Ebulin l is a type-II ribosome-inactivating protein (RIP) isolated from the
leaves of Sambucus ebulus L. As with other type-II RIP, ebulin is a
disulfide-linked heterodimer composed of a toxic A chain and a
galactoside-specific lectin B chain. A normal level of ribosome-inactivating
N-glycosidase activity, characteristic of the A chain of type-II RIP, has been
demonstrated for ebulin l. However, ebulin is considered a nontoxic type-II RIP
due to a reduced cytotoxicity on whole cells and animals as compared with other
toxic type-II RIP like ricin. The molecular cloning, amino acid sequence, and
the crystal structure of ebulin l are presented and compared with ricin. Ebulin
l is shown to bind an A-chain substrate analogue, pteroic acid, in the same
manner as ricin. The galactoside-binding ability of ebulin l is demonstrated
crystallographically with a complex of the B chain with galactose and with
lactose. The negligible cytotoxicity of ebulin l is apparently due to a reduced
affinity for galactosides. An altered mode of galactoside binding in the 2gamma
subdomain of the lectin B chain primarily causes the reduced affinity.
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Selected figure(s)
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Figure 2.
Figure 2. Section of the 2.8-Å electron density for the
trigonal model. A 2Fo-Fc map with sigmaA-weighted phases. The
map is contoured at 1.3  .
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Figure 7.
Figure 7. Comparison of the galactoside-binding, 2  subdomains
of ebulin (top) and ricin (bottom). Galactose is bound to
ebulin. Lactose is bound to ricin. In both pictures, the
galactose moiety is numbered at significant carbons of the sugar
ring. All contacts with lactose in ricin are made with the
galactose moiety. The glucose moiety (GLC) extends into the
solvent. The GLC extension (  -1,4
linkage) from the C1 hydroxyl of the galactose moiety in ricin
is not possible for the C1 hydroxyl of galactose in ebulin,
because of steric interference with 254 N.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2001,
43,
319-326)
copyright 2001.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Hemmi,
A.Kuno,
S.Ito,
R.Suzuki,
T.Hasegawa,
and
J.Hirabayashi
(2009).
NMR studies on the interaction of sugars with the C-terminal domain of an R-type lectin from the earthworm Lumbricus terrestris.
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FEBS J,
276,
2095-2105.
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L.Maveyraud,
H.Niwa,
V.Guillet,
D.I.Svergun,
P.V.Konarev,
R.A.Palmer,
W.J.Peumans,
P.Rougé,
E.J.Van Damme,
C.D.Reynolds,
and
L.Mourey
(2009).
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.
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Proteins,
75,
89.
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PDB codes:
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M.L.DeMarco,
and
R.J.Woods
(2009).
Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces.
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Glycobiology,
19,
344-355.
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A.Bagaria,
K.Surendranath,
U.A.Ramagopal,
S.Ramakumar,
and
A.A.Karande
(2006).
Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin.
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J Biol Chem,
281,
34465-34474.
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PDB codes:
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B.Pils,
R.R.Copley,
and
J.Schultz
(2005).
Variation in structural location and amino acid conservation of functional sites in protein domain families.
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BMC Bioinformatics,
6,
210.
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R.Mikeska,
R.Wacker,
R.Arni,
T.P.Singh,
A.Mikhailov,
A.Gabdoulkhakov,
W.Voelter,
and
C.Betzel
(2005).
Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
17-25.
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PDB codes:
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V.Mishra,
S.Bilgrami,
R.S.Sharma,
P.Kaur,
S.Yadav,
R.Krauspenhaar,
C.Betzel,
W.Voelter,
C.R.Babu,
and
T.P.Singh
(2005).
Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site.
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J Biol Chem,
280,
20712-20721.
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PDB code:
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A.Chambery,
A.Di Maro,
M.M.Monti,
F.Stirpe,
and
A.Parente
(2004).
Volkensin from Adenia volkensii Harms (kilyambiti plant), a type 2 ribosome-inactivating protein.
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Eur J Biochem,
271,
108-117.
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R.Suzuki,
Z.Fujimoto,
A.Kuno,
J.Hirabayashi,
K.Kasai,
and
T.Hasegawa
(2004).
Crystallization and preliminary X-ray crystallographic studies of the C-terminal domain of galactose-binding lectin EW29 from the earthworm Lumbricus terrestris.
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Acta Crystallogr D Biol Crystallogr,
60,
1895-1896.
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T.Uchida,
T.Yamasaki,
S.Eto,
H.Sugawara,
G.Kurisu,
A.Nakagawa,
M.Kusunoki,
and
T.Hatakeyama
(2004).
Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.
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J Biol Chem,
279,
37133-37141.
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PDB code:
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V.Mishra,
A.S.Ethayathulla,
R.S.Sharma,
S.Yadav,
R.Krauspenhaar,
C.Betzel,
C.R.Babu,
and
T.P.Singh
(2004).
Structure of a novel ribosome-inactivating protein from a hemi-parasitic plant inhabiting the northwestern Himalayas.
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Acta Crystallogr D Biol Crystallogr,
60,
2295-2304.
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PDB code:
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F.J.Arias,
P.Antolín,
C.de Torre,
B.Barriuso,
R.Iglesias,
M.A.Rojo,
J.M.Ferreras,
E.Benvenuto,
E.Méndez,
and
T.Girbés
(2003).
Musarmins: three single-chain ribosome-inactivating protein isoforms from bulbs of Muscari armeniacum L. and Miller.
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Int J Biochem Cell Biol,
35,
61-78.
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F.J.Hou,
H.Xu,
and
W.Y.Liu
(2003).
Simultaneous existence of cinnamomin (a type II RIP) and small amount of its free A- and B-chain in mature seeds of camphor tree.
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Int J Biochem Cell Biol,
35,
455-464.
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J.Morlon-Guyot,
M.Helmy,
S.Lombard-Frasca,
D.Pignol,
G.Piéroni,
and
B.Beaumelle
(2003).
Identification of the ricin lipase site and implication in cytotoxicity.
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J Biol Chem,
278,
17006-17011.
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R.P.Kruger,
H.C.Winter,
N.Simonson-Leff,
J.A.Stuckey,
I.J.Goldstein,
and
J.E.Dixon
(2002).
Cloning, expression, and characterization of the Galalpha 1,3Gal high affinity lectin from the mushroom Marasmius oreades.
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J Biol Chem,
277,
15002-15005.
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Y.Bourne,
and
B.Henrissat
(2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
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Curr Opin Struct Biol,
11,
593-600.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
